text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
  //
  // This software is released under a three-clause BSD license:
  //  * Redistributions of source code must retain the above copyright
  //    notice, this list of conditions and the following disclaimer.
  //  * Redistributions in binary form must reproduce the above copyright
  //    notice, this list of conditions and the following disclaimer in the
  //    documentation and/or other materials provided with the distribution.
  //  * Neither the name of any author or any participating institution
  //    may be used to endorse or promote products derived from this software
  //    without specific prior written permission.
  // For a full list of authors, refer to the file AUTHORS.
  // --------------------------------------------------------------------------
  // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
  // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
  // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
  // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
  // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
  // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Hendrik Weisser $
  // $Authors: Hendrik Weisser $
  // --------------------------------------------------------------------------
  
  #pragma once
  
  #include <OpenMS/CHEMISTRY/AASequence.h>
  #include <OpenMS/CHEMISTRY/NASequence.h>
  #include <OpenMS/METADATA/ID/MoleculeParentMatch.h>
  #include <OpenMS/METADATA/ID/ScoredProcessingResult.h>
  
  #include <boost/multi_index_container.hpp>
  #include <boost/multi_index/ordered_index.hpp>
  #include <boost/multi_index/member.hpp>
  
  namespace OpenMS
  {
    namespace IdentificationDataInternal
    {
      /// Identified sequence (peptide or oligonucleotide)
      template <typename SeqType>
      struct IdentifiedSequence: public ScoredProcessingResult
      {
        SeqType sequence;
  
        ParentMatches parent_matches;
  
        explicit IdentifiedSequence(
          const SeqType& sequence,
          const ParentMatches& parent_matches = ParentMatches(),
          const AppliedProcessingSteps& steps_and_scores =
          AppliedProcessingSteps()):
          ScoredProcessingResult(steps_and_scores), sequence(sequence),
          parent_matches(parent_matches)
        {
        }
  
        IdentifiedSequence(const IdentifiedSequence& other) = default;
  
        IdentifiedSequence& operator+=(const IdentifiedSequence& other)
        {
          ScoredProcessingResult::operator+=(other);
          // merge parent matches:
          for (const auto& pair : other.parent_matches)
          {
            auto pos = parent_matches.find(pair.first);
            if (pos == parent_matches.end()) // new entry
            {
              parent_matches.insert(pair);
            }
            else // merge entries
            {
              pos->second.insert(pair.second.begin(), pair.second.end());
            }
          }
  
          return *this;
        }
  
        bool allParentsAreDecoys() const
        {
          if (parent_matches.empty())
          {
            String msg = "no parent found for identified molecule";
            throw Exception::MissingInformation(__FILE__, __LINE__,
                                                OPENMS_PRETTY_FUNCTION, msg);
          }
          for (const auto& pair : parent_matches)
          {
            if (!pair.first->is_decoy) return false;
          }
          return true;
        }
      };
  
      typedef IdentifiedSequence<AASequence> IdentifiedPeptide;
      typedef IdentifiedSequence<NASequence> IdentifiedOligo;
  
      // identified peptides indexed by their sequences:
      typedef boost::multi_index_container<
        IdentifiedPeptide,
        boost::multi_index::indexed_by<
          boost::multi_index::ordered_unique<boost::multi_index::member<
            IdentifiedPeptide, AASequence, &IdentifiedPeptide::sequence>>>
        > IdentifiedPeptides;
      typedef IteratorWrapper<IdentifiedPeptides::iterator> IdentifiedPeptideRef;
  
      // identified oligos indexed by their sequences:
      typedef boost::multi_index_container<
        IdentifiedOligo,
        boost::multi_index::indexed_by<
          boost::multi_index::ordered_unique<boost::multi_index::member<
            IdentifiedOligo, NASequence, &IdentifiedOligo::sequence>>>
        > IdentifiedOligos;
      typedef IteratorWrapper<IdentifiedOligos::iterator> IdentifiedOligoRef;
  
    }
  }
  